--- a/ideas.xml	Thu Aug 24 08:47:27 2017 -0400
+++ b/ideas.xml	Thu Aug 24 09:10:01 2017 -0400
@@ -21,16 +21,16 @@
     #set cell_type_epigenetic_factor = $cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor
     #set specify_genomic_window_cond = $input_type_cond.specify_genomic_window_cond
     #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
-    cp $gen_prep_input_config $prep_input_config &&
+    cp '$gen_prep_input_config' $prep_input_config &&
     prepMat
     $prep_input_config
-    #if str($specify_genomic_window) == 'yes':
+    #if str($specify_genomic_window) == "yes":
         -bed '$specify_genomic_window_cond.bed_input'
     #else:
         -gsz '$chromInfo'
         -wsz $specify_genomic_window_cond.window_size
         #set restrict_chromosomes = $specify_genomic_window_cond.restrict_chromosomes_cond.restrict_chromosomes
-        #if str($restrict_chromosomes) == 'yes':
+        #if str($restrict_chromosomes) == "yes":
             #set chroms = []
             #set chrom_repeat = $specify_genomic_window_cond.restrict_chromosomes_cond.chrom_repeat
             #for $i in $chrom_repeat.chrom
@@ -42,7 +42,7 @@
 #end if
 $bychr
 -c $reads_per_bp
-#if str($blacklist_input) not in ['None', '']:
+#if str($blacklist_input) not in ["None", ""]:
     -exclude '$blacklist_input'
 #end if
 $norm
@@ -65,10 +65,10 @@
 ##############################################
 && ideas
 '$prep_output_config'
-#if str($input_type) == 'datasets':
+#if str($input_type) == "datasets":
     #set specify_genomic_window_cond = $input_type_cond.specify_genomic_window_cond
     #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
-    #if str($specify_genomic_window) == 'yes':
+    #if str($specify_genomic_window) == "yes":
         '$specify_genomic_window_cond.bed_input'
     #else:
         $tmp_dir/*.bed
@@ -77,29 +77,29 @@
     $tmp_dir/*.bed
 #end if
 $hp
-#if str($log2) != '0.0':
+#if str($log2) != "0.0":
     -log2 $log2
 #end if
-#if str($max_states) != '0.0':
+#if str($max_states) != "0.0":
     -G $max_states
 #end if
-#if str($initial_states) != '0':
+#if str($initial_states) != "0":
     -C $initial_states
 #end if
-#if str($max_position_classes) != '0':
+#if str($max_position_classes) != "0":
     -P $max_position_classes
 #end if
-#if str($max_cell_type_clusters) != '0':
+#if str($max_cell_type_clusters) != "0":
     -K $max_cell_type_clusters
 #end if
-#if str($prior_concentration) != '0.0':
+#if str($prior_concentration) != "0.0":
     -A $prior_concentration
 #end if
 -sample $burnin_num $mcmc_num
-#if str($minerr) != '0.0':
+#if str($minerr) != "0.0":
     -minerr $minerr
 #end if
-#if str($maxerr) != '0.0':
+#if str($maxerr) != "0.0":
     -maxerr $maxerr
 #end if
 -thread \${GALAXY_SLOTS:-4}
@@ -110,10 +110,27 @@
 && mv ./*.state $output_state
     ]]></command>
     <configfiles>
-        <configfile name="gen_prep_input_config"><![CDATA[#if str($input_type_cond.input_type) == "datasets" and str($input_type_cond.cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor) == "manual":
-    #for $input_items in $input_type_cond.cell_type_epigenetic_factor_cond.input_repeat:
-${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input}
-    #end for
+        <configfile name="gen_prep_input_config"><![CDATA[#if str($input_type_cond.input_type) == "datasets":
+    #if str($input_type_cond.cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor) == "manual":
+        #for $input_items in $input_type_cond.cell_type_epigenetic_factor_cond.input_repeat:
+    ${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input}
+        #end for
+    #else if str($input_type_cond.cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor) == "extract":
+        #set $cell_type_epigenetic_factor_cond = $input_type_cond.cell_type_epigenetic_factor_cond
+        #set $input_name_positions = $cell_type_epigenetic_factor_cond.input_name_positions
+        #for $i in $cell_type_epigenetic_factor_cond.input:
+            #set $file_name_with_ext = $os.path.basename($i)
+            #set $file_name = $file_name_with_ext.split(".")[0]
+            #if $input_name_positions == "cell_first":
+                #set $cell_type_name = $file_name.split("-")[0]
+                #set $epigenetic_factor_name = $file_name.split("-")[1]
+            #else:
+                #set $cell_type_name = $file_name.split("-")[1]
+                #set $epigenetic_factor_name = $file_name.split("-")[0]
+            #end if
+    ${cell_type_name} ${epigenetic_factor_name} ${i}
+        #end for
+    #end if
 #end if]]></configfile>
     </configfiles>
     <inputs>